Learning statistical models of phenotypes using noisy labeled training data

J Am Med Inform Assoc. 2016 Nov;23(6):1166-1173. doi: 10.1093/jamia/ocw028. Epub 2016 May 12.


Objective: Traditionally, patient groups with a phenotype are selected through rule-based definitions whose creation and validation are time-consuming. Machine learning approaches to electronic phenotyping are limited by the paucity of labeled training datasets. We demonstrate the feasibility of utilizing semi-automatically labeled training sets to create phenotype models via machine learning, using a comprehensive representation of the patient medical record.

Methods: We use a list of keywords specific to the phenotype of interest to generate noisy labeled training data. We train L1 penalized logistic regression models for a chronic and an acute disease and evaluate the performance of the models against a gold standard.

Results: Our models for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.90, 0.89, and 0.86, 0.89, respectively. Local implementations of the previously validated rule-based definitions for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.96, 0.92 and 0.84, 0.87, respectively.We have demonstrated feasibility of learning phenotype models using imperfectly labeled data for a chronic and acute phenotype. Further research in feature engineering and in specification of the keyword list can improve the performance of the models and the scalability of the approach.

Conclusions: Our method provides an alternative to manual labeling for creating training sets for statistical models of phenotypes. Such an approach can accelerate research with large observational healthcare datasets and may also be used to create local phenotype models.

Keywords: Electronic health record; high throughput; machine learning; noisy labels; phenotyping.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Diabetes Mellitus, Type 2
  • Electronic Health Records
  • Humans
  • Logistic Models
  • Machine Learning*
  • Medical Informatics Computing
  • Models, Statistical*
  • Myocardial Infarction
  • Phenotype*
  • Vocabulary, Controlled